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From Oxygen XML Editor/Author

A publishing template can be used for PDF output from the DITA Map PDF - based on HTML5 & CSS transformation scenario.

The Templates tab in the DITA Map PDF - based on HTML5 & CSS transformation scenario dialog displays all the templates that are available in your template gallery. To use a particular template in the transformation scenario, simply select it from this tab and then continue configuring the transformation using the other tabs to suit your needs.

From Command Line

You can use the simpler form, in which you use only the pdf.publishing.template parameter to point to the *.opt (publishing template) file:
dita.bat 
	--input=map\test.ditamap" 
	"-Dpdf.publishing.template=full_path_to_template_dir/my_template.opt" 
	--format=pdf-css-html5 
	...
Or use the two parameters to indicate the folder containing the publishing templates and the name of the publishing template file relative to that folder:
dita.bat 
	--input=map\test.ditamap" 
	"-Dpdf.publishing.template=full_path_to_template_dir" 
	"-Dpdf.publishing.template.descriptor=my_template.opt"
	--format=pdf-css-html5 
	...